Retrieval of crystallographically-derived molecular geometry information
Retrieval of crystallographically-derived molecular geometry information
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DOI：
10.1021/ci049780b
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发表时间：
2004-11-01
期刊：
影响因子：
--
通讯作者：
Orpen, AG
中科院分区：
文献类型：
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作者：
Bruno, IJ;Cole, JC;Orpen, AG
剑桥结构数据库（CSD）中晶体学确定的键长、价角和扭转角信息有许多用途。然而，通过传统的子结构搜索来访问它需要重要的用户干预。因此，这些有价值的数据没有得到充分利用，客户机应用程序无法直接访问这些数据。这种情况已经通过开发一个新的程序（Mogul）得到了改善，该程序可以自动检索CSD中的分子几何数据。该程序使用一个键系统来编码来自CSD结构的片段（键、价角和非环扭）的化学环境。具有相同键的片段被认为是化学相同的，并分组在一起，并分配适当的几何参数（键长）。价角（或扭力角）被计算并存储。使用按键值索引的搜索树，再加上一种新的相似性计算，就可以轻松地找到匹配任何给定查询片段的分布（如果没有足够精确的匹配，则可以找到最接近匹配的分布），而无需用户干预。验证实验表明，除了极少数例外，搜索结果提供分子几何偏好的精确和无偏估计。例如，这种估计可用于验证模型分子库的几何形状或新确定的晶体结构，或协助从低分辨率（例如粉末衍射）x射线数据中获得结构解决方案。
The crystallographic ally determined bond length, valence angle, and torsion angle information in the Cambridge Structural Database (CSD) has many uses. However, accessing it by means of conventional substructure searching requires nontrivial user intervention. In consequence, these valuable data have been underutilized and have not been directly accessible to client applications. The situation has been remedied by development of a new program (Mogul) for automated retrieval of molecular geometry data from the CSD. The program uses a system of keys to encode the chemical environments of fragments (bonds, valence angles, and acyclic torsions) from CSD Structures. Fragments with identical keys are deemed to be chemically identical and are grouped together, and the distribution of the appropriate geometrical parameter (bond length. valence angle, or torsion angle) is computed and stored. Use of a search tree indexed on key values, together with a novel similarity calculation, then enables the distribution matching any given query fragment (or the distributions most closely matching, if an adequate exact match is unavailable) to be found easily and with no user intervention. Validation experiments indicate that, with rare exceptions, search results afford precise and unbiased estimates of molecular geometrical preferences. Such estimates may be used, for example, to validate the geometries of libraries of modeled molecules or of newly determined crystal structures or to assist structure solution from low-resolution (e.g. powder diffraction) X-ray data.